Do Polyphenols Improve Your Gut Bacteria?


This is a guest post written by staff nutritionist Kelsey Marksteiner, RD. Click here to read her blog or join her newsletter!

While you’d be hard-pressed to find anyone who doesn’t think polyphenols are healthy for you, one of the lesser-known benefits of consuming a diet high in polyphenols is its beneficial impact on your gut bacteria.

There are certain substances that have a very significant impact on our gut bacteria balance, like probiotics for example, but other foods and beverages have a smaller, more moderate beneficial effect on our microbiota. Even though these effects are mild, consuming foods and beverages that have beneficial effects on a regular basis is one of the keys to good gut health. Polyphenol-rich foods are excellent to include as part of your overall gut-healing plan along with some of the other heavy-hitters like probiotics and prebiotics. Why? Let’s break it down.

What are Polyphenols?

Polyphenols are naturally-occurring compounds found in in plants. Many of these plants make up our food supply, including fruits, vegetables, coffee, tea, and wine. Once consumed, only about 5-10% of polyphenols are directly absorbed in the small intestine, while the rest make their way to the colon to be broken down by our gut bacteria into metabolites, which then exert their important physiological effects. (1) Researchers are now discovering that the relationship between polyphenols and the gut microbiota is a two way street: that is, the polyphenols change the composition of the gut bacteria, and the gut bacteria are responsible for metabolizing the polyphenols into their bioactive metabolites.

Polyphenols Increase Good Bacteria and Decrease Bad Bacteria

The gut contains over 100 trillion bacteria (that’s ten times the amount of bacteria than we have human cells!) that play a vital role in our overall health. (2) These bacteria are negatively altered by antibiotics, stress, the food we eat, and more, eventually leading to a problem called dysbiosis. Dysbiosis is an imbalance of bacteria that can occur in any of our mucus membranes, such as in the lungs, mouth, nose, and of course, the gut. (3) We’ll be focusing on gut dysbiosis in this article, as it’s something we definitely want to avoid or fix if we’re suffering from digestive problems. Dysbiosis is probably much more common than you’d think: it’s often seen in those with inflammatory bowel disease, fatty liver, obesity, colon cancer, IBS, and more. (4, 5, 6, 7, 8) One of the best things we can do for our digestive (and overall) health is balance our gut bacteria. Luckily, there are plenty of ways for us to do that and consuming polyphenols is one of them!

Polyphenols seem to act as a prebiotic-type substance, meaning that they increase the amount of healthy bacteria in the gut, such as Lactobacillus and Bifidobacteria strains. Tea is possibly the most researched out of all the high-polyphenol foods, with many studies proving the prebiotic effects of tea extracts, leaves and polyphenol compounds. (9, 10, 11, 12, 13) Compared to those not treated with polyphenols, rats consuming red wine polyphenols have completely different predominant bacteria: those not consuming polyphenols showed predominantely Bacteroides, Clostridium and Propionibacterium species, while polyphenol-treated rats had mostly Bacteroides, Lactobacillus and Bifidobacterium species, showing that polyphenol intake can make quite an impact on gut bacteria. (14) In a study on humans, a wild blueberry drink significantly increases Lactobacillus counts. (15) Here’s the best news you’ll hear today: red wine also contains polyphenols that seem to have a similarly beneficial impact on gut bacteria. (16) Pretty sure that sentence made this article worth reading, didn’t it? It gets even better: cocoa also has prebiotic activity. (17) While this article isn’t meant to give you an excuse to go on a wine and chocolate free-for-all, it does mean that consuming these foods in moderation is likely beneficial for your gut flora.

Not only do polyphenols increase counts of beneficial bacteria, they also inhibit growth of potentially pathogenic bacteria. Catechin, a polyphenol found in tea, chocolate, apples, and blackberries (to name a few), has been shown to significantly inhibit proliferation of Clostridium histolyticum, a pathogenic bacteria. (18) Phenolic compounds contained in various berries have also been studied, showing antimicrobial effects on human pathogens such as Staphylococcus and Salmonella. (19) Studies also show that tea phenolics consumption repress the growth of Clostridium perfringens, Clostridium difficile, and Bacteroides spp. (20)

Include Polyphenol-Rich Foods for Balanced Gut Flora

By now you understand that it’s not just probiotics that can make a big difference in the balance of your gut bacteria. Eating polyphenol-rich foods on a regular basis, along with probiotics, prebiotics, and resistant starch will balance your microbiotia and get you on your way to good gut health! You will of course want to exclude any polyphenol-rich foods that you are sensitive to, but otherwise include as many as you’d like! There’s more research to be done in this area, and we don’t know all the ways that each different polyphenol affects us, so it’s best to consume a variety of polyphenol-rich foods for the best results. To get you started, below is a list of the Top 40 Paleo Polyphenol-Rich Foods from highest in polyphenols to lowest per serving. (21) Note that not all foods have been tested for their polyphenol content, so this list only includes those that have been studied. You can check out the polyphenol content of a food here, in case you’re wondering about one not on the list!

Top 40 Polyphenol-Rich Foods:

  • Black elderberry
  • Black chokeberry
  • Black currant
  • Blueberry
  • Globe artichoke heads
  • Coffee
  • Sweet cherry
  • Strawberry
  • Blackberry
  • Plum
  • Raspberry
  • Flaxseed meal
  • Dark chocolate
  • Chestnut
  • Black tea
  • Green tea
  • Apple
  • Hazelnut
  • Red wine
  • Black grape
  • Black olive
  • Spinach
  • Pecan
  • Prune
  • Red currant
  • Peach
  • Green olive
  • Red onion
  • Green grape
  • Potato
  • Shallot
  • Red chicory
  • Broccoli
  • Nectarine
  • Pear
  • Yellow onion
  • Apricot
  • Asparagus
  • Almond
  • White wine


kelseyrd03This is a guest post written by Kelsey Marksteiner, RD. Kelsey is a Registered Dietitian with a Bachelors degree in Nutrition from NYU and a Master’s in Human Nutrition and Functional Medicine. She works in private practice and recommends individualized dietary therapy focusing on biologically appropriate diet principles to aid her clients in losing weight, gaining energy, and pursuing continued health. She is a firm believer that everyone is different, and she tailors her plan for each and every individual. Through her work, she aims to meld the dietary wisdom of traditional cultures with the latest science in integrative and functional medicine to create plans for her clients that work in the modern world. You can learn more about Kelsey on her staff bio page, or by visiting her private practice website. Join her newsletter here!

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Comments Join the Conversation

  1. Lynnette Foster-Horwith says

    Well it seems like a jump to say that since polyphenols are in wine etc that then wine is ok when alcohol is a sugar e.g.

  2. says

    Great article (thanks guys). What really needs to be mentioned (and hasn’t been) is that wild plants have higher phenolic content than their corresponding cultivated plants. This is confirmed in many different studies. Therefore, if you want to receive the most polyphenols, you should strive to eat wild-gathered foods (rather than cultivated foods). This is not to say that organic produce isn’t healthful, but wild plants have a deeper nutrition (again, that comment can be supported by study) and have intact phytochemistry (i.e., it hasn’t been bred out of them), resulting in more polyphenols, which in addition to the benefits to gut bacteria, provide higher antioxidant values.

    I realize that most people are consuming store-purchased foods and, therefore, a general focus is placed on cultivated produce by most authors. However, this has created a general ignorance (I don’t mean for that to sound rude) of the value of wild plants and why people should learn to forage or otherwise secure wild plants in their diets (when possible). After all, humans have consumed exclusively wild plants for most of their existence. Best wishes.

  3. PC says

    A warning about flax seed – it isn’t often mentioned, but it is thyroid suppressing (google it). I have noticed this whenever I use it – I don’t feel very well afterwards at all.

  4. says

    Our gut is as unique as our finger print, most of us know that pre/probiotics benefit our gut, but few realize that polyphenols also benefit the healthy flora of our gastrointestinal system. Very good information here and thanks for sharing.

  5. Sara says

    Question: Are frozen fruits as high as fresh in polyphenols (organic frozen) ? What about dried elderberries? The local beer and wine shop sells dried (or possibly freeze dried) elderberries that I’ve been wanting to re-hydrate to cook into a syrup. Is this ok or should I look for a different source? When I was growing up we had a huge elderberry bush (vine?) next to my uncle’s farm that my mom would make elderberry pie from-so good! Unfortunately, the county road crews came through and sprayed to kill it all-what a waste!

  6. Lauri Salmi says

    Thanks for the article Kelsey!

    I have hypoglycemia, early morning insomnia and some adrenal fatigue. I’m wondering why i’m very sensitive to many nutrients. For example i lose sleep the following night if i consume chocolate at any point of day, probiotics, hcl, salt, avocados, sweet potatoes, salmon, alcohol. And all the supplements that affect the brain or adrenals (C,B,licorice,adaptogens,some amino acids) have very strong effects even with small doses.

    My gut functions normally but i suspect some bacterial imbalance. Might the sensitivity be caused by leaky gut or leaky blood brain barrier?

    • PC says

      This could be nervous system based, perhaps? The gut and brain definitely interact, but if you have AF and hypos it sounds like your mind is under a lot of stress. Perhaps accupuncture, meditation, breathing techniques might be helpful?

      I have similar issues, and having accupuncture recently really helped me!

    • Robert Gellibolian says

      @danjon and Jamal
      This is complex question. The short answer is that it depends on the polyphenol in question. As you may know, there are 1,000s of molecules with a polyphenolic chemical structure, with 100s identified in edible plants.

      Let’s look at isoflavones as an example. These are flavonoids which are structurally similar to estrogens (FYI: can bind to the estrogen receptor…important in women). They are mainly found in soya products. They come in various conjugated forms: aglycone, plus various glucosides. Some in the latter class are very sensitive to heat and can be modified to their glycoside derivatives. The fermentation of certain foods during processing (e.g., tempeh or miso) results in the conversion of the glycoside to the aglycone forms. These aglycone forms are highly resistant to heat.

      Flavonols (another class ) are present monomeric (e.g., catechins) or complex polymeric form (proanthocyanidins). They can be found in wine, but are highest in tea and chocolate. Compared to flavonoids above, flavanols are not glycosylated in foods and can be remarkably stable in heat (as long as the pH is acidic).

      So, to make a long (and complex) story short, the answer is: It depends. My opinion is not to worry about it too much. Eat a variety and diverse source of fruits and veggies and let your gut flora and biology figure out the rest. You’ll be fine.

      Happy eating,

  7. Paul says

    I’m still trying to get my head around the fact that there are ten fold more life forms living within and on our own singular form. We are totally out numbered in this universe and completely dependent, but since we have a thinking brain we think we are special and superior. We may be nothing but a constillation or amalgam of organisms collecsed by conscienceness.

  8. zane says

    Could a moderate amount of red wine still have a beneficial impact for someone who has dysbiosis and or digestion problems? Or should they fix any gut related problems before reintroducing red wine?
    I heard someone say alcohol could be detrimental for gut bacteria. I am not sure what type or amount of alcohol they were referring to, or if they were referring only to people with compromised gut health to begin with.

  9. Wenchypoo says

    Is this different from the bacteria that potato starch is supposed to feed, or are they the same? Should I drop one for the other, or do them both?

  10. Jamal Jafri says

    I read somewhere that processing involved in chocolate making destroys, or significantly reduces, polyphenols that were originally present. Is this true? Also, are there any cooking methods that have more adverse effect than others, and is the chemical integrity of polyphenols affected by the presence or absence of other common ingredients such as sugar, oil or lemon juice?

  11. AnnieLaurie Burke says

    OK, no red wine, coffee, and chocolate binges. But perhaps a little less guilt about moderate use of these foods is in order. But how about a blueberry, artichoke, pecan, etc. free-for-all ;-)? I was amazed to see how many of the foods/drinks I love and eat often are in the top 40. Maybe that’s why I enjoy excellent digestive health 99+% of the time.

  12. says

    What do you think about products like Amazing Grass that are raw green powders with very high ORAC values? Obviously real whole foods are preferable but interested in their usefulness here nonetheless, thanks!

  13. barbara says

    To what extent does processing (heating, canning, turning cocoa into a candy bar, etc.) have on the foods’ polyphenols?

  14. Anne says

    Thank you for this informative article. I saw that you mentioned mouth dysbiosis. I never see anything on this, so if you could please talk about it in detail, I’d really appreciate it!

  15. Ali says

    Hi there,

    Can you recommend any good polyphenol supplements? I can’t have any sugar (including fruit) or caffiene and I struggle with digesting vegetables, so mainly stick to root vegetables. I have severe gut dysbiosis and have been trying to heal my gut for the past 7 months but have hit a wall. I wonder if a polyphenol supplement, without the sugar, would help me?

    • Claudia says

      I am in almost the same boat (seem to be ok again with berries, as well as some veggies at this point). Try the R.W. Knudsen Black Current Juice (unsweetened). It is very tart and intense, best when watered down. It is very delicious.

  16. Lynn says

    Thank you Kelsey. You have listed such a great list of polyphenols, what would be good prebiotics, probiotics, and resistant starch and in what combination should you eat them? Great information.

  17. Michael Chekanski says

    Great news!!! Let’s go on a dark chocolate and red wine binge!!! Just kidding; but I now have more motivation to take the red wine over the cider and grab a bar of dark chocolate over refined desserts.

  18. says

    One thing I truly like about this site is that Chris and his collaborators are always pouring through the latest research.

    I recently have also been reading about how much our bodies are affected by gut microbia, and therefore the importance of cultivating beneficial bacteria.

    Chris was one of many Paleo advocates who criticized some studies that declared meat eating to be unhealthy due to the Trimethylamine N-oxide (“TMAO”) created by a particular type of gut bacteria when digesting the carnitine in red meat — a bacteria present in meat eaters, but not vegetarians, said the studies.

    TMAO is a common organic compound found in animals, and is thought to increase the risk of heart disease ten times greater than cholesterol.

    But what was not investigated was to what extent eating polyphenols and other foods that feed beneficial microbiota would do overwhelm TMAO-producing bacteria.

    Moreover, this gut bacteria topic doesn’t end with TMAO, but it now thought to link to chronic inflammation, a precursor to a whole host of degenerative disease states.

    For more on this, check out “Can The Right Gut Bacteria Fight Obesity And Slay Metabolic Syndrome?” here


    • Tiffany says

      This is fascinating. I have been eating a strict Paleo diet to manage my leaky gut from being celiac. I’ve had to drop all grains, even gf grains, dairy (casein allergy) and now eggs. So Paleo was essential to rebuilding my system. But I have been unhappy, especially since I have a sweet tooth. I take a couple of probiotics because they do wonders for my system. After learning about resistant starch, I decided to test eating banana, blueberry and a smidge of maple syrup for breakfast. Sometimes combined with smoked salmon. Since having this I’ve seen a dramatic improvement in my digestion. We eat a meat-protein rich lunch and a protein-based evening snack along with a fiber-rich green smoothie in the vitamix for dinner. It was only when I stopped eating morning chicken and switched to the fruit that I started seeing weight loss, and we work out 5-6 days a week. I was seeing such great results from this change, I stopped needing afternoon yerba mate (50% caffeine). I am much more awake in the morning now. Given the sugar in the fruit, and the maple syrup, I thought this wouldn’t work. But it does. And the addition of a little sweet makes my mood much better.

      • April Ellis says

        Have you read the book “Breaking the Vicious Cycle” by Elaine Gottschall? It is in regards to the Specific Carbohydrate Diet which focuses on monosacchrides and the ability to digest ONLY monosacchrides in people with IBS, Celiac, Crohn’s, etc… Adding in that little bit of glucose may be why you are feeling better and still able to eat those foods without side effects. :)

  19. Kari says

    I have a history of digestive problems but coffee, tea and dark chocolate have always felt good in my stomach. Glad to have a scientific explanation. Nice article.

  20. Victoria Chandler says

    I can’t drink green tea or take anything that has a green tea extract added because within 20 mins I will vomit. I can drink black tea with milk and I can drink herbal teas (which I enjoy tremendously) but green tea is a definite no-no for me. I did read that it was probably one of the catechins that some people are sensitive too, the EGCG (?) I believe. If it was just polyphenols or flavonoids then other foods with these in would have the same effect, but it is only the green tea that makes me feel ill.

      • Cat says

        Well, if it was the salicylates, then she would also be reacting to other foods with vomiting, so it seems unlikely.

        EGCG is found in higher concentrations in green tea, compared to black tea, along with other catechins (a type of polyphenol). Black tea is also fermented. Herbal teas aren’t really teas, because they don’t use the tea plant.

        • Lou says

          Not necessarily Cat. It might be the unique features of tea, *including the extremely high salicylate content*. I respond to the salicylates in tea much stronger than in any other source – save dried fruits. In any case, if overly sensitive to tea it is worth it to check out salicylate sensitivity – is my main point. It occurs more than most people think, and can lead to a host of complaints. I hope Chris will look more into it.

  21. says

    Always soaking up support for my love of coffee!

    I am curious (because I also make a point to regularly consume Kombucha, Kraut & Kimchi – for the probiotic support ) … which do you believe is more effective for promoting healthy gut – the polyphenols or the fermented foods & beverages ?

    • says

      I think they are both very important. However, since most people tend to eat less fermented foods than they do foods high in polyphenols you hear fermented foods touted as a “superfood” more often. I think they’re both incredibly important to consume on a regular basis!

      • says

        I couldn’t agree with you more. One other thing that I always advocate for people to think about when eating fermented food is that the probiotics in those foods will invariably modify the polyphenolic content in those foods. As you eloquently mentioned in your post, only 5% of the polyphenols are absorbed in the small intestine…the other 95% is unavailable for absorption and thus ends up in the colon, where they either 1) undergo modification to simpler phenolic acids, which are much better absorbed by the body, or 2) they are excreted through the feces and do nothing.

        This is important for folks suffering from gut dysbiosis.


  22. says

    Why do some people have cross reactivity with things like chocolate, coffee and potatoes that can mimic gluten if there is a substantial amount of polyphenols in those foods?

  23. Lou says

    I just want to add a caveat with regard to tea – mentioned here as ‘possibly the most researched out of all the high-polyphenol foods with many studies proving the prebiotic effects of tea extracts – and other foods that are not just rich in polyphenols but are also very high in salicylates. Salicylates can, in sensitive individuals – exacerbate or even cause ibs (-like) symptoms (as well as a host of other symptoms, including hair loss). I didn’t improve on any of the typical ibs/sibo diets until i started lowering my salicylate count considerable, which included, sadly, ceasing all camellia sinensis consumption. So be forewarned, people, polyphenols may be very healthy and good for your gut flora – foods rich in these compounds may also be rich in salicylates, and cause serious trouble for your gut.

      • prioris says

        Looking at the symptoms, I wonder if a fungal infection may be at the root of salicylates sensitivity.

        The effect of toxins in our system is that they will likely make people more sensitive or allergic to other things. When enough of the GMO food toxin known as Bt-toxin gets into the body, it will cause people to react to or become allergic to other foods. Fungal infections can release toxins.

    • Amy says

      My daughter is Celiac with salicylate sensitivity. Blueberries, honey, peppermint, even shampoo set her body off. Phenols aren’t for everyone…

  24. David Churchill says

    How does pomegranate juice not make this list? From the studies I have seen on polyphenols pomegranates are at or near the top always.

  25. says

    Can’t get too much information about polyphenols, because of the tremendous variety of different contributing elements and secondly we still don’t know half of what it is exactly that they’re involved in. Hormesis? Activating immune system?
    I miss in the list the tart cherry (newer dark shrub varieties) which rates among the very top. The same holds for the newest jewel Haskap (Lonicera) or edible honey berry, which outstrips even the blueberry and blackberry

    • Honora says

      This stuff grows wild on the West Coast of the South Island of New Zealand as Himalayan honeysuckle. I wonder if it is the same species. Must google it and find out if it’s edible.

  26. Craig says

    Can’t tell from this article whether Lactobacillus is supposed to be good or bad – increased by red wine, decreased by blueberries. Well …. it’s the (warm fuzzy) thought that counts.

  27. Matt says

    Very informative.
    There’s been quite a buzz about polyphenols recently.
    Is there a specific supplement that you recommend?

    • says

      Great article. This goes along with Dr. Art Ayers work but said in a more lay person fashion.

      It was stated:

      “Red wine also contains polyphenols that seem to have a similarly beneficial impact on gut bacteria. (16) Pretty sure that sentence made this article worth reading, didn’t it?”

      “Seems to have?” What does that mean?

      And I thought that alcohol destroyed our good bacteria and damages the gut lining even in small amounts. Am I mistaken?

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